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External Resources

Discussion Boards

Knowing where to look for advice can be an important part of problem solving in bioinformatics.

The following websites & discussion boards are well populated with experienced people across a wide variety of topics in programming, mathematics & bioinformatics, and can be a very helpful first port of call when you're stuck.

Data Storage

The Research Data Storage Infrastructure (RDSI) Project Link to external website is an initiative of the National Collaborative Research Infrastructure Strategy, is funded from the Education Investment Fund under the Super Science (Future Industries) initiative. Secure Data Storage is available upon request.

GitHub

The Bioinformatics Hub has a GitHub account Link to external website which contains much of our public analytic code. Hopefully this is an informative site for those who look through our work.

Computing Resources

Most research performed by the Bioinformatics Hub utilises the Phoenix HPC cluster located within the University of Adelaide.

Visit the Phoenix High Performance Computing for more information, or to sign up for an account. Training workshops in the usage of this resource are also run regularly, so please check the Training & Workshops page for the next scheduled session

    Software Downloads

    Some key bioinformatics tools & their sources are:

    Statistical Software

    Packages in current development by the Bioinformatics Hub

    • ngsReports Link to external website: Easier R handling of multiple NGS reporting files, such as FASTQC output and log files from common alignment tools
    • strandCheckR Link to external website: Check strandedness of RNA Seq alignments. Also able to be used for removal of genomic DNA sequences for libraries with incomplete DNA removal

    Tools for NGS Data

    If you are unsure about the installation or use of any NGS tools, please email the Bioinformatics Hub to see if we can help.

    Many NGS tools are now able to be installed using Git. An installation Link to external website is available for all platforms is available.

    Data Handling

    • BAMTools Link to external website - For easy handling of BAM files.
    • BEDTools Link to external website - a software package for manipulating BED files, with some utilities working with BAM. Built upon BAMTools.
    • Cutadapt Link to external website - for trimming adapter sequences from NGS reads
    • GATK Link to external website - the Genome Analysis Toolkit. Rich funtionality including an accurate SNP caller. Built upon Picard.
    • SAMTools Link to external website - various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
    • sambamba Link to external website - Faster implementations of many SAMTools functions
    • Picard Link to external website - a suite of java-based tools for data exploration

    Sequence Alignment

      • BWA Link to external website - Burrows-Wheeler Aligner for short and long reads.
      • Bowtie Link to external website - Highly efficient short read aligner. Natively support SAM output in recent version.
      • HISAT2 Link to external website - The main RNA-Seq aligner used by the Boinformatics Hub
      • TopHat Link to external website - for mapping short RNA-seq reads bridging exon junctions.
      • STAR Link to external website- An RNA-Seq aligner implemented in parallel for additional speed

      Other Helpful Tools

      • FASTQC Link to external website - A quality control tool for high throughput sequence data.
      • Galaxy Link to external website - is an online collection of NGS tools accessible via a Graphical User Interface (GUI) for those with minimal command-line experience
        Bioinformatics Hub
        Address

        Level 4,
        Santos Petroleum Engineering Building,
        North Terrace Campus
        The University of Adelaide
        SA 5005
        Australia

        Contact

        T: +61 8 8313 1207
        Email